This study simulates the Wigner Effect of nuclear-grade graphite in a High Temperature Gas-cooled Reactor (HTGR). The graphite was artificially irradiated with 3 MeV C2+ ions to mimic the fast neutron-radiation damage of the HTGR core environment. The irradiation temperatures were controlled between the range of 500–800 °C in a high vacuum environment of 10−7 torr. This high-dosage radiation creates enormous amounts of Frenkel pairs, which induce lattice swelling. These Frenkel vacancies and interstitials generate new strain fields and, hence, store energy in the distorted crystalline structure. The structural integrity of nuclear grade graphite was quantified using high-resolution transmission electron microscopy (HRTEM). The microstructure was estimated by the fast Fourier transform of HRTEM images. Within the samples irradiated with 10 dpa at 600 °C, the d-spacing of {0 0 0 2} expanded from 0.336 nm to 0.396 nm accompanying with the greatest distorted graphite microstructure. The c-axis of graphite swelled approximately 18% and the disorder coefficient was 1.10 ± 0.17 (1/nm). The synchrotron X-ray experimental results, gauged from 500 μm3 volume, suggesting that the ion-implanted graphite only deformed locally and epitaxially. This study also presents possible mechanisms.